@Diane_
"Therefore, is the simplest solution to just use the $5500 hospital payment receipt (in 2021) as the evidence of the full costs in 2021 (since that amount was legitimate at the time), if I am audited by the IRS?"
This is acceptable under the circumstances. However, since you now have a 2022 refund, you need to apply that to your 2022 medical expenses. If you have paid $6000 so far, $3900 is covered by the refund (which represents tax-free HSA money) so only $2100 remains eligible for future reimbursement from your HSA or as a medical expense deduction.
" (received in 2022 directly back to HSA account)"
This is new information to us. By depositing the money in the HSA without going through the "return of excess distribution" procedure, it is a regular contribution. Once money hits your checking account or wallet, it loses any uniqueness based on it's source and it's all just money. You paid $6000 to the hospital so far and you contributed $3900 to the HSA. You can't say "but that $3900 is not a contribution, its a return" because the bank refuses to process it as a return and you just made a contribution. (In fact, if you made the deposit first, that's probably part of the reason why they are refusing to treat it as a return, because you had to set that up in advance.)
"Does that $3900 reimbursement now count as an official HSA contribution for 2022, even though the money was originally contributed in 2021"
If you deposited the money into the HSA and the bank did not accept it as a return, then it is a new contribution. Remember, it's all just money. You got a withdrawal, you made a deposit. If you didn't or couldn't follow the rules for a return of excess distribution, then it's just a contribution and you may need to reduce your payroll contributions (or stop them early) so you don't exceed your limit for 2022.
